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Detailed information for vg1111945410:

Variant ID: vg1111945410 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11945410
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTTTTTACTATAAACAGAAAAATCCTTAATTGAATTATTGCGCAATAAATAAATCCCGGGAGAGAGAGAGGGGCGGCGCCGACATGCGGGCCCCACAT[G/A]
GCAGTGACTCGGGGGGGCGGTTCACGGTGGACCGAGTCCACGGACCGGGGAAGGCGCGGTGCACCATGTGGCGCTGACGTGGCGCCGACGCGGCGGCCAC

Reverse complement sequence

GTGGCCGCCGCGTCGGCGCCACGTCAGCGCCACATGGTGCACCGCGCCTTCCCCGGTCCGTGGACTCGGTCCACCGTGAACCGCCCCCCCGAGTCACTGC[C/T]
ATGTGGGGCCCGCATGTCGGCGCCGCCCCTCTCTCTCTCCCGGGATTTATTTATTGCGCAATAATTCAATTAAGGATTTTTCTGTTTATAGTAAAAACAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.50%	20.50%	32.04%	0.00%	NA
All Indica	2759	23.50%	27.20%	49.29%	0.00%	NA
All Japonica	1512	95.60%	1.90%	2.58%	0.00%	NA
Aus	269	8.60%	58.70%	32.71%	0.00%	NA
Indica I	595	18.50%	17.50%	64.03%	0.00%	NA
Indica II	465	20.60%	26.70%	52.69%	0.00%	NA
Indica III	913	27.50%	33.60%	38.88%	0.00%	NA
Indica Intermediate	786	24.30%	27.50%	48.22%	0.00%	NA
Temperate Japonica	767	96.70%	1.00%	2.22%	0.00%	NA
Tropical Japonica	504	92.90%	3.40%	3.77%	0.00%	NA
Japonica Intermediate	241	97.50%	1.20%	1.24%	0.00%	NA
VI/Aromatic	96	89.60%	8.30%	2.08%	0.00%	NA
Intermediate	90	46.70%	25.60%	27.78%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111945410	G -> A	LOC_Os11g20610.1	downstream_gene_variant ; 1235.0bp to feature; MODIFIER	silent_mutation	Average:46.409; most accessible tissue: Minghui63 young leaf, score: 70.038	N	N	N	N
vg1111945410	G -> A	LOC_Os11g20600-LOC_Os11g20610	intergenic_region ; MODIFIER	silent_mutation	Average:46.409; most accessible tissue: Minghui63 young leaf, score: 70.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111945410	NA	1.16E-08	mr1806	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	2.37E-08	mr1829	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	5.24E-06	mr1842	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	1.47E-07	mr1062_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	5.44E-06	mr1169_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	1.08E-11	mr1806_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	7.33E-07	mr1806_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	2.81E-09	mr1829_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1111945410	NA	1.44E-07	mr1842_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251